EMPIAR-11746 - FIB-SEM dataset of a human bone osteosarcoma epithelial cell (U2-OS) [1168 micrographs in TIFF format]

EMPIAR-11746

FIB-SEM dataset of a human bone osteosarcoma epithelial cell (U2-OS) [1168 micrographs in TIFF format]

Publication:

Accelerating data sharing and reuse in volume electron microscopy

Czymmek KJ, Belevich I, Bischof J, Mathur A, Collinson L, Jokitalo E

Nature cell biology 26 (2024) 498-503

PMID: 38609529

DOI: 10.1038/s41556-024-01381-3

Related EMDB entry:

Deposited:

2023-10-25

Released:

2024-02-15

Last modified:

2024-06-05

Imageset size:

5.20 GB

Imageset DOI:

10.6019/EMPIAR-11746

Experimental metadata:

Download xml json

Contains:

micrographs - single frame

Image Sets

1. Aligned and pre-processed FIB-SEM dataset of a human bone osteosarcoma epithelial cell (U2-OS)

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

1168

Image size:

(3394, 1385)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(25.0, 25.0)

Details:

Z-step is 50Å
Voxels: 0.0025 x 0.0025 x 0.005 um
16bit raw images taken with EsB and InLens-SE detectors were fused as 70%+30%. The datasets were aligned and processed in Microscopy Image Browser (https://mib.helsinki.fi/)

Files:

Archives and downloads the selected files into an uncompressed zip file.

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

Browse All Files

Quick Links

Browse EMPIAR

Sample Preparation Widget

Volume Browser

Tomo Viewer Prototype

Claim entries to your ORCiD

Talks and Tutorials

EMPIAR Quick tour

Publications

Re-use study

Statistics

EMPIAR in the news

COVID-19 Data Portal

EMDB

BioImage Archive

PDBe

EMNavigator@PDBj

PDBj

Citations

prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.

He L, Bartesaghi A. (2026)

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

Jones HN, Deshmukh A, Pande K. (2026)

CryoGS: High-Quality Cryo-EM Homogeneous Reconstruction by Gaussian Splatting

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

Point cloud deformation modeling for particle selection following cryo-EM 2D classification.

Wang X, Mo Z, Li F, Zhang F, Wan X. (2026)

ICECREAM: high-fidelity equivariant cryo-electron tomography.

Kishore V, Debarnot V, Righetto RD, Engel BD, Dokmanić I. (2026)

CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection.

Schäfer JH, Calza A, Hom K, Damodar P, Peng R, Bogdanović N, Lander GC, Stagg SM, Cianfrocco MA. (2025)